rs6526555

Variant names:

• chrX-26351782-A-C
• rs6526555

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.406 in 110,829 control chromosomes in the GnomAD database, including 8,109 homozygotes. There are 13,218 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (8109 hom., 13218 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.406 AC: 44953 AN: 110774 Hom.: 8099 Cov.: 23 AF XY: 0.399 AC XY: 13167 AN XY: 33034

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.399

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 45017 AN: 110829 Hom.: 8109 Cov.: 23 AF XY: 0.399 AC XY: 13218 AN XY: 33099

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.402

Alfa AF: 0.281 Hom.: 10939

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6526555; hg19: chrX-26369899;